Genetics and Genomics of the Genus Amycolatopsis

Abstract

Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies.

The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata

“…This may reflect the large levels of detritus accumulated by this plant [56]. Also, Amycolatopsis species have previously been reported to contribute to plant health by antibiotic production [57]. The genus Mycobacterium, which contains important human pathogens [58], was also prevalent in rhizosphere soils.…”

Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains

“…Within the actinomycetes, the genus Streptomyces is the most prolific and most studied producer of secondary metabolites, but members of the families Pseudonocardiaceae and Micromonosporaceae have also shown to produce a broad diversity of bioactive molecules. Among Pseudonocardiaceae , members of the genus Amycolatopsis produce several relevant secondary metabolites, such as balhimycin, vancomycin, avoparcin, ristomycin, chelocardin, chloroeremomycin, ECO-0501 and rifamycin (Chen et al, 2016 ; Kumari et al, 2016 ). More recently, other antibiotics have been described from some Amycolatopsis strains such as macrotermycins A–D (Beemelmanns et al, 2017 ), pargamicins B–D (Hashizume et al, 2017 ) and rifamorpholines A–E (Xiao et al, 2017 ).…”

Integrating Vectors for Genetic Studies in the Rare ActinomyceteAmycolatopsis marina

“…Previous studies in rare Actinomycete species have largely focused on the use of the well-characterised ϕC31-based integration vectors, and have mostly overlooked tools based on other phage integrases(43-45). Additionally, the conjugation methods used widely in Streptomyces gene transfer because of their ease have shown little success in rare Actinomycetes, including species in the genus Amycolatopsis , so electroporation has been the long-preferred method of gene transfer for species in this genus(5, 9, 46, 47). However, the growing interest in the use of serine integrases for synthetic biology applications(11) has led to further research into expanding the pool of available enzymes and their potentials as genetic tools(48-50).…”

“…The publicly available NCBI database contains nearly 70 genomes of Amycolatopsis strains, covering more than 40 species from this genus. Similar to Streptomyces , the genome of each Amycolatopsis contains, on average, over 20 secondary metabolic gene clusters(9). The mining of these metabolic clusters offers great potential for novel antibiotic discovery.…”